Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	Gene Summary
	Phenotypic Information (metabolism pathway, cancer, disease, phenome)
	Mutations : SVs, CNVs, SNVs
	Gene expression: GE, Protein, DEGE, CNV vs GE
	Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG
	Pharmacological Information: Drug-Gene Network
	Cross referenced IDs

Gene Summary for PCYT1B

Basic gene info.	Gene symbol	PCYT1B
	Gene name	phosphate cytidylyltransferase 1, choline, beta
	Synonyms	CCTB\|CTB
	Cytomap	UCSC genome browser: Xp22.11
	Genomic location	chrX :24576203-24665455
	Type of gene	protein-coding
	RefGenes	NM_001163264.1, NM_001163265.1,NM_004845.4,
	Ensembl id	ENSG00000102230
	Description	CCT BCCT-betaCT BCTP:phosphocholine cytidylyltransferase bcholine-phosphate cytidylyltransferase Bphosphorylcholine transferase B
	Modification date	20141207
dbXrefs	MIM : 604926
	HGNC : HGNC
	Ensembl : ENSG00000102230
	HPRD : 05376
	Vega : OTTHUMG00000021270
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PCYT1B
	BioGPS: 9468
	Gene Expression Atlas: ENSG00000102230
	The Human Protein Atlas: ENSG00000102230
Pathway	NCI Pathway Interaction Database: PCYT1B
	KEGG: PCYT1B
	REACTOME: PCYT1B
	ConsensusPathDB
	Pathway Commons: PCYT1B
Metabolism	MetaCyc: PCYT1B
	HUMANCyc: PCYT1B
Regulation	Ensembl's Regulation: ENSG00000102230
	miRBase: chrX :24,576,203-24,665,455
	TargetScan: NM_001163264
	cisRED: ENSG00000102230
Context	iHOP: PCYT1B
	cancer metabolism search in PubMed: PCYT1B
	UCL Cancer Institute: PCYT1B
Assigned class in ccmGDB	C

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Phenotypic Information for PCYT1B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PCYT1B
	Familial Cancer Database: PCYT1B

* This gene is included in those cancer gene databases.


Oncogene ¹	Tumor Suppressor gene ²	Cancer Gene Census ³	CancerGenes ⁴	Network of Cancer Gene ⁵	Significant driver gene in	Therapeutic Vulnerabilities in Cancer¹

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
KEGG_GLYCEROPHOSPHOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: PCYT1B
	MedGen: PCYT1B (Human Medical Genetics with Condition)
	ClinVar: PCYT1B
Phenotype	MGI: PCYT1B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PCYT1B

Mutations for PCYT1B

* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PCYT1B related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
AI952718	PCYT1B	13	287	X	24668190	24676354	GALNT1	281	404	18	33270975	33271098
AI656193	PCYT1B	13	287	X	24668190	24676354	GALNT1	281	404	18	33270975	33271098

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

There's no copy number variation information in COSMIC data for this gene.

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SNV Counts per Each Loci in COSMIC data : go to COSMIC point mutation

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=39)	Stat. for Synonymous SNVs (# total SNVs=5)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

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Top 10 SNVs Having the Most Samples in COSMIC data

* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.

GRCh37 position	Mutation(aa)	Unique sampleID count
chr23:24597510-24597510	p.R211C	3
chr23:24625952-24625952	p.D82N	2
chr23:24608208-24608208	p.R140C	2
chr23:24608226-24608226	p.E134K	2
chr23:24608151-24608151	p.E159K	2
chr23:24580566-24580566	p.Q318H	1
chr23:24625868-24625868	p.V110L	1
chr23:24637174-24637174	p.D49N	1
chr23:24608167-24608167	p.L153L	1
chr23:24580574-24580574	p.P316S	1

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SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample		3	1	7	1				2			6	3				5	3		4
# mutation		3	1	6	1				2			6	3				5	3		5
nonsynonymous SNV		3	1	5	1				2			4	2				4	2		4
synonymous SNV				1								2	1				1	1		1

cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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Top 10 SNVs Having the Most Samples in TCGA data

* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.

Genomic Position	Mutation(aa)	Unique sampleID count
chrX:24608140	p.K144N,PCYT1B	2
chrX:24580609	p.D186V,PCYT1B	1
chrX:24608151	p.R60I,PCYT1B	1
chrX:24625952	p.S185S,PCYT1B	1
chrX:24580619	p.R57K,PCYT1B	1
chrX:24608156	p.S156F,PCYT1B	1
chrX:24625963	p.C37C,PCYT1B	1
chrX:24593333	p.R328G	1
chrX:24608167	p.T33T,PCYT1B	1
chrX:24625972	p.E350G,PCYT1B	1

Other DBs for Point Mutations

Point Mutation Table of Ensembl: go to Ensembl variation table

Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

Copy Number for PCYT1B in TCGA

* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.

cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for PCYT1B

Gene Expression in Cancer Cell-lines (CCLE)

* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

Differential Gene Expression in Primary Tumors (TCGA)

* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))

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CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

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Gene-Gene Network Information

Co-Expressed gene's network Plot

* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types


AIPL1,BCL2L14,BYSL,CCDC67,E2F3,ETV6,GPM6B, GPR161,JAKMIP2,NR2E1,P2RX3,PAQR9,PCYT1B,SOHLH2, tAKR,TAS1R1,TET1,TTLL8,UCHL1,USP49,ZNF705D	ARHGAP19,CACNA1C,COL17A1,COL4A5,COL4A6,GRIA4,ITGA2, NEO1,NFASC,PCYT1B,PTPRT,RARB,SDK2,SEMA5A, SEPT3,SHC4,SLC27A6,SRGAP3,SV2A,ZNF561,ZNF648

ATP1B2,BAI3,C14orf132,CEND1,CNTN2,DCAF12L2,GPR88, GRIA1,HMP19,KCNK3,MLLT11,NACAD,PCYT1B,PDZD4, RGAG4,RND2,SALL2,SLC22A17,TAGLN3,TCEAL5,TMEFF2	ACTG2,ACTN1,AOC3,ATP1A2,BVES,CALD1,CNN1, CTXN1,DACT3,FAM46B,FLNA,RBFOX3,ITGB3,NLGN1, PCYT1B,PDLIM7,PYGM,SGCD,SLC8A2,TAGLN,ZFHX4

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for PCYT1B

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00122	phosphate cytidylyltransferase 1, choline, beta	approved; nutraceutical	Choline

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Cross referenced IDs for PCYT1B

* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information